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- PDB-3f6w: XRE-family like protein from Pseudomonas syringae pv. tomato str.... -

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Basic information

Entry
Database: PDB / ID: 3f6w
TitleXRE-family like protein from Pseudomonas syringae pv. tomato str. DC3000
ComponentsXRE-family like protein
KeywordsDNA BINDING PROTEIN / helix-turn-helix / xenobiotic response element family of transcriptional regulators / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsPetrova, T. / Cuff, M. / Shackleford, G. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: XRE-family like protein from Pseudomonas syringae pv. tomato str. DC3000
Authors: Petrova, T. / Cuff, M. / Shackleford, G. / Gu, M. / Joachimiak, A.
History
DepositionNov 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XRE-family like protein
B: XRE-family like protein
C: XRE-family like protein
D: XRE-family like protein
E: XRE-family like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6516
Polymers46,4415
Non-polymers2091
Water10,575587
1
A: XRE-family like protein
hetero molecules

A: XRE-family like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9954
Polymers18,5772
Non-polymers4182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2150 Å2
ΔGint-6 kcal/mol
Surface area9420 Å2
MethodPISA
2
A: XRE-family like protein
B: XRE-family like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7863
Polymers18,5772
Non-polymers2091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-6 kcal/mol
Surface area8780 Å2
MethodPISA
3
B: XRE-family like protein

D: XRE-family like protein


Theoretical massNumber of molelcules
Total (without water)18,5772
Polymers18,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area1480 Å2
ΔGint-12 kcal/mol
Surface area9290 Å2
MethodPISA
4
C: XRE-family like protein
E: XRE-family like protein


Theoretical massNumber of molelcules
Total (without water)18,5772
Polymers18,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-12 kcal/mol
Surface area9150 Å2
MethodPISA
5
C: XRE-family like protein
D: XRE-family like protein


Theoretical massNumber of molelcules
Total (without water)18,5772
Polymers18,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-7 kcal/mol
Surface area8490 Å2
MethodPISA
6
E: XRE-family like protein

E: XRE-family like protein


Theoretical massNumber of molelcules
Total (without water)18,5772
Polymers18,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2180 Å2
ΔGint-6 kcal/mol
Surface area7950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.196, 48.306, 111.424
Angle α, β, γ (deg.)90.00, 98.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-116-

HOH

21A-513-

HOH

31A-618-

HOH

DetailsUnknown. Likely to be a dimer

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Components

#1: Protein
XRE-family like protein / DNA-binding protein


Mass: 9288.284 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: PSPTO0717, PSPTO_0717 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q889N2
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 3M Sodium chloride, 1M Bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935, 0.97948
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979481
ReflectionResolution: 1.85→44.659 Å / Num. obs: 78813 / % possible obs: 99.2 % / Redundancy: 7.5 % / Biso Wilson estimate: 23.91 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 30.4
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4 / Num. unique all: 2670 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXDphasing
SHELXEmodel building
MLPHAREDMphasing
SOLVEphasing
RESOLVEmodel building
ARP/wARPmodel building
CCP4model building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→44.659 Å / SU ML: 0.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 3944 5 %
Rwork0.1905 --
obs0.1934 78813 99.18 %
all-78813 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.917 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 38.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 14 587 3748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfond0.006
X-RAY DIFFRACTIONfngle0.852
X-RAY DIFFRACTIONflanarity0.003
X-RAY DIFFRACTIONfhirality0.055
X-RAY DIFFRACTIONfihedral13.816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8505-1.87310.30941280.25462555X-RAY DIFFRACTION95
1.8731-1.89680.3221350.23392729X-RAY DIFFRACTION99
1.8968-1.92170.27541260.2172619X-RAY DIFFRACTION98
1.9217-1.94810.29231570.2122615X-RAY DIFFRACTION99
1.9481-1.97590.28731370.21292657X-RAY DIFFRACTION99
1.9759-2.00540.26751600.21262703X-RAY DIFFRACTION99
2.0054-2.03670.29031160.21892672X-RAY DIFFRACTION99
2.0367-2.07010.23631210.19832647X-RAY DIFFRACTION99
2.0701-2.10580.26091380.1992730X-RAY DIFFRACTION99
2.1058-2.14410.23761440.20462647X-RAY DIFFRACTION99
2.1441-2.18530.27851590.20122656X-RAY DIFFRACTION99
2.1853-2.22990.30041340.18652695X-RAY DIFFRACTION99
2.2299-2.27840.24821370.18432641X-RAY DIFFRACTION99
2.2784-2.33140.22241480.16772723X-RAY DIFFRACTION99
2.3314-2.38970.24591280.17832654X-RAY DIFFRACTION99
2.3897-2.45430.22831500.18122695X-RAY DIFFRACTION99
2.4543-2.52650.26631550.1912658X-RAY DIFFRACTION100
2.5265-2.60810.27321310.19212660X-RAY DIFFRACTION100
2.6081-2.70130.26551320.20712770X-RAY DIFFRACTION100
2.7013-2.80940.29081510.21942633X-RAY DIFFRACTION100
2.8094-2.93730.26031350.21362680X-RAY DIFFRACTION100
2.9373-3.09210.24651400.20012709X-RAY DIFFRACTION100
3.0921-3.28580.24741440.1922697X-RAY DIFFRACTION100
3.2858-3.53940.21691160.16652698X-RAY DIFFRACTION100
3.5394-3.89530.18941400.15842720X-RAY DIFFRACTION100
3.8953-4.45860.24261690.15292663X-RAY DIFFRACTION100
4.4586-5.61560.21061750.15682652X-RAY DIFFRACTION100
5.6156-44.67150.22931380.20712691X-RAY DIFFRACTION99

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